Mismatch repair in Xenopus egg extracts: DNA strand breaks act as signals rather than excision points.

In Xenopus egg extracts, DNA strand breaks (nicks) located 3' or 5' to a mismatch cause an overall 3-fold stimulation of the repair of the mismatch in circular heteroduplex DNA molecules. The increase in mismatch repair is almost entirely due to an increase in repair of the nicked strand, which is stimulated 5-fold. Repair synthesis is centered to the mismatch site, decreases symmetrically on both sides, and its position is not significantly altered by the presence of the nick. Therefore, it appears that in the Xenopus germ cells, the mismatch repair system utilizes nicks as signals for the induction and direction of mismatch repair, but not as the start or end point for excision and resynthesis.

Host-parasite dynamics and outgrowth of virus containing a single K70R amino acid change in reverse transcriptase are responsible for the loss of human immunodeficiency virus type 1 RNA load suppression by zidovudine.

The association between human immunodeficiency virus type I (HIV-1) RNA load changes and the emergence of resistant virus variants was investigated in 24 HIV-1-infected asymptomatic persons during 2 years of treatment with zidovudine by sequentially measuring serum HIV-1 RNA load and the relative amounts of HIV-1 RNA containing mutations at reverse transcriptase (RT) codons 70 (K-->R), 41 (M-->L), and 215 (T-->Y/F). A mean maximum decline in RNA load occurred during the first month, followed by a resurgence between 1 and 3 months, which appeared independent of drug-resistance. Mathematical modeling suggests that this resurgence is caused by host-parasite dynamics, and thus reflects infection of the transiently increased numbers of CD4+ lymphocytes. Between 3 and 6 months of treatment, the RNA load returned to baseline values, which was associated with the emergence of virus containing a single lysine to arginine amino acid change at RT codon 70, only conferring an 8-fold reduction in susceptibility. Despite the relative loss of RNA load suppression, selection toward mutations at RT codons 215 and 41 continued. Identical patterns were observed in the mathematical model. While host-parasite dynamics and outgrowth of low-level resistant virus thus appear responsible for the loss of HIV-1 RNA load suppression, zidovudine continues to select for alternative mutations, conferring increasing levels of resistance.

Chemical egg defense in a green lacewing (Ceraeochrysa smithi)

The green lacewing Ceraeochrysa smithi (Neuroptera, Chrysopidae), like other members of its family, lays its eggs on stalks, but it is unusual in that it coats these stalks with droplets of an oily fluid. The liquid consists of a mixture of fatty acids, an ester, and a series of straight-chain aldehydes. Relative to the eggs of a congeneric chrysopid that lacks stalk fluid, the eggs of C. smithi proved well protected against ants. Components of the fluid, in an assay with a cockroach, proved potently irritant. Following emergence from the egg, C. smithi larvae imbibe the stalk fluid, thereby possibly deriving nutritive benefit, defensive advantage, or both.

DNA-protein binding assays from a single sea urchin egg: a high-sensitivity capillary electrophoresis method.

A capillary electrophoresis method has been developed to study DNA-protein complexes by mobility-shift assay. This method is at least 100 times more sensitive than conventional gel mobility-shift procedures. Key features of the technique include the use of a neutral coated capillary, a small amount of linear polymer in the separation medium, and use of covalently dye-labeled DNA probes that can be detected with a commercially available laser-induced fluorescence monitor. The capillary method provides quantitative data in runs requiring < 20 min, from which dissociation constants are readily determined. As a test case we studied interactions of a developmentally important sea urchin embryo transcription factor, SpP3A2. As little as 2-10 x 10(6) molecules of specific SpP3A2-oligonucleotide complex were reproducibly detected, using recombinant SpP3A2, crude nuclear extract, egg lysates, and even a single sea urchin egg lysed within the capillary column.

A Drosophila seminal fluid protein, Acp26Aa, stimulates egg laying in females for 1 day after mating.

Mating triggers behavioral and physiological changes in the Drosophila melanogaster female, including an elevation of egg laying. Seminal fluid molecules from the male accessory gland are responsible for initial behavioral changes, but persistence of these changes requires stored sperm. Using genetic analysis, we have identified a seminal fluid protein that is responsible for an initial elevation of egg laying. This molecule, Acp26Aa, has structural features of a prohormone and contains a region with amino acid similarity to the egg-laying hormone of Aplysia. Acp26Aa is transferred to the female during mating, where it undergoes processing. Here we report the generation and analysis of mutants, including a null, in Acp26Aa. Females mated to male flies that lack Acp26Aa lay fewer eggs than do mates of normal males. This effect is apparent only on the first day after mating. The null mutation has no other detectable physiological or behavioral effects on the male or the mated female.

Short-term Load Forecasting Using Neural Network For Future Smart Grid Application

Short-term load forecasting of power system has been a classic problem for a long time. Not merely it has been researched extensively and intensively, but also a variety of forecasting methods has been raised. This thesis outlines some aspects and functions of smart meter. It also presents different policies and current statuses as well as future projects and objectives of SG development in several countries. Then the thesis compares main aspects about latest products of smart meter from different companies. Lastly, three types of prediction models are established in MATLAB to emulate the functions of smart grid in the short-term load forecasting, and then their results are compared and analyzed in terms of accuracy. For this thesis, more variables such as dew point temperature are used in the Neural Network model to achieve more accuracy for better short-term load forecasting results.

Nutrient Load Reduction: Challenges facing the Chesapeake 2000 Agreement

The Chesapeake Bay is the largest estuary in the United States supporting a complex ecosystem that sustains many habitats and the organisms that depend on them. The bay also supports economic, recreational, and cultural activities to over 16 million people residing in the watershed. Changes within the watershed have caused excessive levels of nutrients, mainly nitrogen and phosphorous, to pollute the bay. The Chesapeake Bay Program, guided by a complex agreement, was created to address these and other issues and oversee the restoration of the bay. The most recent version of this agreement, the Chesapeake 2000, declares its continued commitment to restore the bay with over 100 goals to be met by the year 2010. Reports show that although intensive efforts have been made to promote nutrient reduction, very little reduction has actually resulted. This project described these efforts. The final results reveal obstacles affecting progress, shortcomings to current approaches and possible solutions for future implementation.

Sequencing and functional analysis of the genome of a nematode egg-parasitic fungus, Pochonia chlamydosporia

Pochonia chlamydosporia is a worldwide-distributed soil fungus with a great capacity to infect and destroy the eggs and kill females of plant-parasitic nematodes. Additionally, it has the ability to colonize endophytically roots of economically-important crop plants, thereby promoting their growth and eliciting plant defenses. This multitrophic behavior makes P. chlamydosporia a potentially useful tool for sustainable agriculture approaches. We sequenced and assembled ∼41 Mb of P. chlamydosporia genomic DNA and predicted 12,122 gene models, of which many were homologous to genes of fungal pathogens of invertebrates and fungal plant pathogens. Predicted genes (65%) were functionally annotated according to Gene Ontology, and 16% of them found to share homology with genes in the Pathogen Host Interactions (PHI) database. The genome of this fungus is highly enriched in genes encoding hydrolytic enzymes, such as proteases, glycoside hydrolases and carbohydrate esterases. We used RNA-Seq technology in order to identify the genes expressed during endophytic behavior of P. chlamydosporia when colonizing barley roots. Functional annotation of these genes showed that hydrolytic enzymes and transporters are expressed during endophytism. This structural and functional analysis of the P. chlamydosporia genome provides a starting point for understanding the molecular mechanisms involved in the multitrophic lifestyle of this fungus. The genomic information provided here should also prove useful for enhancing the capabilities of this fungus as a biocontrol agent of plant-parasitic nematodes and as a plant growth-promoting organism.